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comparison gene_fraction/src/alignment_util.h @ 0:f95150c37d38 draft default tip

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planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
author chrisd
date Sun, 21 Feb 2016 23:31:55 -0500
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-1:000000000000 0:f95150c37d38
1 #ifndef ALIGNMENT_UTIL_H
2 #define ALIGNMENT_UTIL_H
3
4 #include <string>
5 #include <vector>
6
7 #include <boost/algorithm/string.hpp>
8
9 #include "int_util.h"
10
11 // macro to check if read mapped
12 #define READ_UNMAPPED 4
13
14 /**
15 * Splits alignment into separate parts
16 */
17 std::vector<std::string> split_alignment(std::string &alignment) {
18 std::vector<std::string> parts;
19
20 boost::trim_if(alignment, boost::is_any_of("\t "));
21 // split on tab delimeter
22 boost::split(parts, alignment, boost::is_any_of("\t "), boost::token_compress_on);
23
24 return parts;
25 }
26
27 /**
28 * Validates bit flag
29 */
30 bool is_good_flag(const int &bit_flag) {
31 if( (bit_flag & READ_UNMAPPED) > 0) return false;
32 return true;
33 }
34
35 /**
36 * Validates rname
37 */
38 bool is_good_rname(const std::string &rname) {
39 return rname.compare("*") != 0;
40 }
41
42 /**
43 * Validates pos
44 */
45 bool is_good_pos(const int &pos) {
46 return pos > 0;
47 }
48
49 /**
50 * Validates cigar
51 */
52 bool is_good_cigar(const std::string &cigar) {
53 return cigar.compare("*") != 0;
54 }
55
56 /**
57 * Validates seq
58 */
59 bool is_good_seq(const std::string &seq) {
60 return seq.compare("*") != 0;
61 }
62
63 /**
64 * Validates alignment fields
65 */
66 bool fields_are_good(std::vector<std::string> &parts) {
67 int bit_flag = s_to_i(parts[1]);
68 int pos = s_to_i(parts[3]);
69
70 std::string rname = parts[2];
71 std::string cigar = parts[5];
72 std::string seq = parts[9];
73
74 if(!(is_good_flag(bit_flag))) return false;
75 if(!(is_good_pos(pos))) return false;
76 if(!(is_good_rname(rname))) return false;
77 if(!(is_good_cigar(cigar))) return false;
78 if(!(is_good_seq(seq))) return false;
79
80 return true;
81 }
82
83 /**
84 * Stores alignments that pass validity checks
85 */
86 bool is_good_alignment(std::string &alignment) {
87 std::vector<std::string> alignment_parts;
88
89 alignment_parts = split_alignment(alignment);
90
91 if(!(fields_are_good(alignment_parts)))
92 return false;
93 return true;
94 }
95
96 #endif /* ALIGNMENT_UTIL_H */